- Introduction to metabolomics
- Preprocessing of LC-MS data in Bioconductor
12 July 2018
readMSData (MSnbase package):xcms: findChromPeaks function, passing settings along with an algorithm-specific parameter object.cwp <- CentWaveParam(peakwidth = c(2, 10), snthresh = 5) data <- findChromPeaks(data, param = cwp) head(chromPeaks(data), n = 3)
## mz mzmin mzmax rt rtmin rtmax into intb ## [1,] 114.0907 114.0899 114.0929 1.954 0.280 3.907 1559.829 1555.923 ## [2,] 114.0913 114.0884 114.0929 5.860 4.465 8.650 1890.221 1885.757 ## [3,] 114.0914 114.0899 114.0929 10.882 8.650 13.114 1950.953 1946.210 ## maxo sn sample is_filled ## [1,] 584.9510 584 1 0 ## [2,] 601.8881 601 1 0 ## [3,] 691.9580 691 1 0
TODO add content: - image describing the alignment - available methods - what is the result? (m/z - rt ranges).
TODO add content: - what sources of variation? - Crucial to add QC controls in the experiment. - available methods (RUV, linear models). - MS runs not very expensive, running replicates, QC controls etc usually not a problem.
TODO add content: - What databases available - up and coming: compound db, similar to ensembldb and alike. Problem: unclear license situation.
MSnbase).xcms.